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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.25

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-11-21, 23:29 UTC based on data in: /home/mf019/longread_pangenome/expanded_dataset_analysis


        General Statistics

        Showing 0/157 rows and 8/8 columns.
        Sample NameN50 (Kbp)Assembly Length (Mbp)# contigs# bases# CDS% Borreliella burgdorferi% Top 5 Species% Unclassified
        B331PP
        903.7Kbp
        1.4Mbp
        19
        1409078
        1379
        B331PP-checkpoint
        19
        1409078
        1379
        B418PP
        902.8Kbp
        1.4Mbp
        18
        1376853
        1336
        B500PP
        903.7Kbp
        1.4Mbp
        19
        1429303
        1402
        ESI26H
        910.4Kbp
        1.3Mbp
        64
        1276481
        1213
        ESI36H
        909.9Kbp
        1.2Mbp
        11
        1182078
        1118
        ESI403H
        910.4Kbp
        1.4Mbp
        34
        1364813
        1338
        ESI425H
        342.8Kbp
        1.3Mbp
        21
        1260215
        1199
        GCA_002151465.1_ASM215146v1_genomic
        909.9Kbp
        1.3Mbp
        12
        1288112
        1274
        GCA_002151485.1_ASM215148v1_genomic
        910.7Kbp
        1.3Mbp
        11
        1301554
        1305
        GCA_002151505.1_ASM215150v1_genomic
        909.9Kbp
        1.3Mbp
        13
        1341182
        1339
        GCA_002442595.2_ASM244259v2_genomic
        903.7Kbp
        1.4Mbp
        19
        1409089
        1379
        GCA_003367295.1_ASM336729v1_genomic
        908.5Kbp
        1.3Mbp
        16
        1280240
        1237
        GCA_019134655.1_ASM1913465v1_genomic
        910.0Kbp
        1.2Mbp
        11
        1217256
        1168
        GCA_019464575.1_ASM1946457v1_genomic
        903.7Kbp
        1.4Mbp
        19
        1429304
        1405
        GCA_024662155.1_ASM2466215v1_genomic
        903.2Kbp
        1.4Mbp
        18
        1392060
        1357
        GCA_024662175.1_ASM2466217v1_genomic
        920.8Kbp
        1.4Mbp
        18
        1417706
        1400
        GCA_024662195.1_ASM2466219v1_genomic
        909.7Kbp
        1.5Mbp
        21
        1513701
        1505
        GCA_030439605.1_ASM3043960v1_genomic
        910.7Kbp
        1.0Mbp
        4
        1007753
        919
        GCA_030439625.1_ASM3043962v1_genomic
        910.4Kbp
        1.0Mbp
        4
        1007827
        918
        GCA_030439665.1_ASM3043966v1_genomic
        902.8Kbp
        1.0Mbp
        4
        1000122
        915
        GCA_030440345.1_ASM3044034v1_genomic
        907.8Kbp
        1.0Mbp
        4
        1006065
        918
        GCA_030444985.1_ASM3044498v1_genomic
        910.6Kbp
        1.0Mbp
        4
        1007632
        917
        GCA_030445005.1_ASM3044500v1_genomic
        910.4Kbp
        1.0Mbp
        4
        1007828
        918
        GCA_030445025.1_ASM3044502v1_genomic
        910.7Kbp
        1.0Mbp
        4
        1008124
        919
        GCA_030445065.1_ASM3044506v1_genomic
        910.2Kbp
        1.0Mbp
        4
        1006503
        920
        GCA_032595375.1_ASM3259537v1_genomic
        909.6Kbp
        1.0Mbp
        4
        1007086
        922
        GCA_032595515.1_ASM3259551v1_genomic
        911.4Kbp
        1.0Mbp
        4
        1004596
        903
        GCA_032595535.1_ASM3259553v1_genomic
        909.7Kbp
        1.0Mbp
        4
        1005759
        907
        GCA_032595755.1_ASM3259575v1_genomic
        910.1Kbp
        1.0Mbp
        4
        1006563
        882
        GCA_038801875.1_ASM3880187v1_genomic
        920.0Kbp
        0.9Mbp
        2
        946504
        846
        GCA_040790715.1_ASM4079071v1_genomic
        908.7Kbp
        1.3Mbp
        14
        1289159
        1216
        GCA_040790735.1_ASM4079073v1_genomic
        909.5Kbp
        1.4Mbp
        18
        1391486
        1359
        GCA_040790745.1_ASM4079074v1_genomic
        902.8Kbp
        1.4Mbp
        18
        1371468
        1331
        GCA_040790755.1_ASM4079075v1_genomic
        902.7Kbp
        1.3Mbp
        16
        1321156
        1300
        GCA_040790765.1_ASM4079076v1_genomic
        910.1Kbp
        1.4Mbp
        19
        1397896
        1369
        GCA_040790775.1_ASM4079077v1_genomic
        907.6Kbp
        1.4Mbp
        17
        1417953
        1383
        GCA_040790785.1_ASM4079078v1_genomic
        910.0Kbp
        1.4Mbp
        18
        1383845
        1347
        GCA_040790795.1_ASM4079079v1_genomic
        916.8Kbp
        1.3Mbp
        16
        1325608
        1251
        GCA_040790805.1_ASM4079080v1_genomic
        907.9Kbp
        1.2Mbp
        12
        1216633
        1169
        GCA_040819585.1_PFhe_I_PB_Ill_cons_genomic
        910.3Kbp
        1.3Mbp
        15
        1341511
        1317
        GCF_000008685.2_ASM868v2_genomic
        910.7Kbp
        1.5Mbp
        22
        1521208
        1508
        GCF_000021405.1_ASM2140v1_genomic
        906.7Kbp
        1.3Mbp
        15
        1345494
        1327
        GCF_000166635.1_ASM16663v1_genomic
        902.2Kbp
        1.3Mbp
        17
        1339539
        1311
        GCF_000166655.1_ASM16665v1_genomic
        922.8Kbp
        1.5Mbp
        21
        1531091
        1519
        GCF_000171735.2_ASM17173v2_genomic
        85.3Kbp
        1.5Mbp
        27
        1453013
        1441
        GCF_000172295.2_ASM17229v2_genomic
        35.7Kbp
        1.3Mbp
        53
        1344204
        1302
        GCF_000172315.2_ASM17231v2_genomic
        83.1Kbp
        1.3Mbp
        26
        1294354
        1252
        GCF_000172335.2_ASM17233v2_genomic
        169.2Kbp
        1.5Mbp
        24
        1485884
        1475
        GCF_000181555.2_ASM18155v2_genomic
        908.8Kbp
        1.5Mbp
        32
        1469834
        1418
        GCF_000181575.2_ASM18157v2_genomic
        171.0Kbp
        1.3Mbp
        20
        1321434
        1306
        GCF_000181715.2_ASM18171v2_genomic
        169.5Kbp
        1.3Mbp
        25
        1295451
        1255
        GCF_000181855.2_ASM18185v2_genomic
        37.0Kbp
        1.4Mbp
        54
        1427907
        1411
        GCF_002151465.1_ASM215146v1_genomic
        909.9Kbp
        1.3Mbp
        12
        1288112
        1274
        GCF_002151485.1_ASM215148v1_genomic
        910.7Kbp
        1.3Mbp
        11
        1301554
        1305
        GCF_002151505.1_ASM215150v1_genomic
        909.9Kbp
        1.3Mbp
        13
        1341182
        1339
        GCF_002442595.2_ASM244259v2_genomic
        903.7Kbp
        1.4Mbp
        19
        1409089
        1379
        GCF_003367295.1_ASM336729v1_genomic
        908.5Kbp
        1.3Mbp
        16
        1280240
        1237
        GCF_019134655.1_ASM1913465v1_genomic
        910.0Kbp
        1.2Mbp
        11
        1217256
        1168
        GCF_019464575.1_ASM1946457v1_genomic
        903.7Kbp
        1.4Mbp
        19
        1429304
        1405
        GCF_024662155.1_ASM2466215v1_genomic
        903.2Kbp
        1.4Mbp
        18
        1392060
        1357
        GCF_024662175.1_ASM2466217v1_genomic
        920.8Kbp
        1.4Mbp
        18
        1417706
        1400
        GCF_024662195.1_ASM2466219v1_genomic
        909.7Kbp
        1.5Mbp
        21
        1513701
        1505
        GCF_040790715.1_ASM4079071v1_genomic
        908.7Kbp
        1.3Mbp
        14
        1289159
        1216
        GCF_040790735.1_ASM4079073v1_genomic
        909.5Kbp
        1.4Mbp
        18
        1391486
        1359
        GCF_040790745.1_ASM4079074v1_genomic
        902.8Kbp
        1.4Mbp
        18
        1371468
        1331
        GCF_040790755.1_ASM4079075v1_genomic
        902.7Kbp
        1.3Mbp
        16
        1321156
        1300
        GCF_040790765.1_ASM4079076v1_genomic
        910.1Kbp
        1.4Mbp
        19
        1397896
        1369
        GCF_040790775.1_ASM4079077v1_genomic
        907.6Kbp
        1.4Mbp
        17
        1417953
        1383
        GCF_040790785.1_ASM4079078v1_genomic
        910.0Kbp
        1.4Mbp
        18
        1383845
        1347
        GCF_040790795.1_ASM4079079v1_genomic
        916.8Kbp
        1.3Mbp
        16
        1325608
        1251
        GCF_040790805.1_ASM4079080v1_genomic
        907.9Kbp
        1.2Mbp
        12
        1216633
        1169
        GCF_040819585.1_PFhe_I_PB_Ill_cons_genomic
        910.3Kbp
        1.3Mbp
        15
        1341511
        1317
        K89HH
        274.3Kbp
        1.5Mbp
        150
        1557782
        1479
        UCT109H
        910.6Kbp
        1.5Mbp
        28
        1476377
        1438
        UCT110H
        906.8Kbp
        1.4Mbp
        114
        1417187
        1343
        UCT113H
        905.8Kbp
        1.3Mbp
        253
        1304891
        1189
        82.6%
        83.8%
        1.2%
        UCT113H_kraken2
        82.6%
        83.8%
        1.2%
        UCT124H
        900.9Kbp
        1.5Mbp
        50
        1510565
        1476
        UCT29H
        910.5Kbp
        1.6Mbp
        24
        1559716
        1547
        UCT30H
        905.5Kbp
        1.5Mbp
        89
        1471861
        1385
        83.1%
        85.4%
        1.1%
        UCT30H_kraken2
        83.1%
        85.4%
        1.1%
        UCT31H
        910.6Kbp
        1.5Mbp
        32
        1531745
        1514
        UCT32H
        921.1Kbp
        1.5Mbp
        57
        1501989
        1459
        86.0%
        86.0%
        1.8%
        UCT32H_kraken2
        86.0%
        86.0%
        1.8%
        UCT35H
        910.0Kbp
        1.3Mbp
        33
        1350407
        1278
        78.8%
        87.9%
        9.1%
        UCT35H_kraken2
        78.8%
        87.9%
        9.1%
        UCT50H
        902.8Kbp
        1.3Mbp
        90
        1341231
        1284
        72.2%
        77.8%
        4.4%
        UCT50H_kraken2
        72.2%
        77.8%
        4.4%
        UCT92H
        906.7Kbp
        1.5Mbp
        62
        1537760
        1512
        95.2%
        96.8%
        1.6%
        UCT92H_kraken2
        95.2%
        96.8%
        1.6%
        UCT95H
        893.6Kbp
        1.5Mbp
        15
        1491903
        3042
        UCT96H
        900.9Kbp
        1.5Mbp
        35
        1481271
        1451
        UNY1032P
        910.6Kbp
        1.5Mbp
        18
        1459435
        1428
        UNY1038P
        915.7Kbp
        1.4Mbp
        19
        1403595
        1354
        UNY1083P
        923.1Kbp
        1.4Mbp
        226
        1494188
        1405
        56.2%
        56.6%
        30.5%
        UNY1083P_kraken2
        56.2%
        56.6%
        30.5%
        UNY1085P
        903.4Kbp
        1.4Mbp
        18
        1409080
        1350
        UNY1090P
        912.7Kbp
        1.4Mbp
        19
        1413250
        1377
        UNY1128P
        213.8Kbp
        1.4Mbp
        277
        1488312
        1399
        75.8%
        76.2%
        5.1%
        UNY1128P_kraken2
        75.8%
        76.2%
        5.1%
        UNY149P
        915.7Kbp
        1.4Mbp
        19
        1427032
        1389
        UNY169P
        902.8Kbp
        1.3Mbp
        17
        1346761
        1303
        UNY172P
        903.4Kbp
        1.4Mbp
        16
        1352494
        1298
        UNY193P
        910.1Kbp
        1.4Mbp
        19
        1403883
        1358
        UNY203P
        910.1Kbp
        1.3Mbp
        17
        1326072
        1289
        UNY208P
        912.7Kbp
        1.4Mbp
        19
        1413253
        1376
        UNY990P
        902.8Kbp
        1.4Mbp
        17
        1367194
        1301
        URI101H
        910.5Kbp
        1.6Mbp
        32
        1554475
        1513
        URI102H
        910.6Kbp
        1.4Mbp
        44
        1442774
        1392
        URI103H
        921.1Kbp
        1.5Mbp
        56
        1474413
        1424
        URI107H
        910.6Kbp
        1.5Mbp
        49
        1505434
        1479
        URI111H
        910.6Kbp
        1.5Mbp
        23
        1539609
        1513
        URI112H
        903.1Kbp
        1.4Mbp
        85
        1431440
        1366
        82.4%
        85.9%
        2.4%
        URI112H_kraken2
        82.4%
        85.9%
        2.4%
        URI117H
        434.9Kbp
        1.4Mbp
        160
        1384478
        1299
        84.4%
        85.6%
        1.2%
        URI117H_kraken2
        84.4%
        85.6%
        1.2%
        URI118H
        921.0Kbp
        1.4Mbp
        109
        1380118
        1317
        URI120H
        910.7Kbp
        1.6Mbp
        105
        1576195
        1544
        URI33H
        902.8Kbp
        1.3Mbp
        44
        1353948
        1272
        90.9%
        93.2%
        2.3%
        URI33H_kraken2
        90.9%
        93.2%
        2.3%
        URI34H
        910.1Kbp
        1.4Mbp
        79
        1376021
        1295
        84.8%
        86.1%
        1.3%
        URI34H_kraken2
        84.8%
        86.1%
        1.3%
        URI36H
        927.7Kbp
        1.5Mbp
        53
        1482383
        1423
        73.6%
        90.6%
        7.5%
        URI36H_kraken2
        73.6%
        90.6%
        7.5%
        URI39H
        920.7Kbp
        1.6Mbp
        28
        1557202
        1542
        URI40H
        910.6Kbp
        1.5Mbp
        82
        1509727
        1470
        72.0%
        76.8%
        1.2%
        URI40H_kraken2
        72.0%
        76.8%
        1.2%
        URI41H
        914.4Kbp
        1.5Mbp
        84
        1468867
        1437
        URI42H
        910.6Kbp
        1.5Mbp
        74
        1460998
        1422
        URI44H
        921.1Kbp
        1.4Mbp
        75
        1417636
        1341
        76.0%
        81.3%
        1.3%
        URI44H_kraken2
        76.0%
        81.3%
        1.3%
        URI45H
        42.8Kbp
        1.5Mbp
        350
        1585394
        1458
        81.1%
        84.0%
        0.9%
        URI45H_kraken2
        81.1%
        84.0%
        0.9%
        URI46H
        906.8Kbp
        1.4Mbp
        95
        1437550
        1363
        87.4%
        90.5%
        1.1%
        URI46H_kraken2
        87.4%
        90.5%
        1.1%
        URI47H
        921.2Kbp
        1.5Mbp
        29
        1512039
        1477
        URI48H
        902.8Kbp
        1.4Mbp
        22
        1377993
        1323
        95.5%
        95.5%
        4.5%
        URI48H_kraken2
        95.5%
        95.5%
        4.5%
        URI56H
        903.3Kbp
        1.3Mbp
        230
        1297641
        1187
        URI86H
        919.1Kbp
        1.4Mbp
        88
        1406230
        1329
        URI87H
        910.6Kbp
        1.5Mbp
        66
        1505755
        1466
        URI88H
        906.7Kbp
        1.5Mbp
        33
        1540602
        1502
        URI89H
        910.7Kbp
        1.5Mbp
        85
        1553229
        1526
        74.1%
        77.6%
        1.2%
        URI89H_kraken2
        74.1%
        77.6%
        1.2%
        URI91H
        910.7Kbp
        1.6Mbp
        26
        1588266
        1574
        URI93H
        910.6Kbp
        1.5Mbp
        29
        1474340
        1426
        UWI247P
        912.3Kbp
        1.4Mbp
        17
        1359286
        1300
        UWI248P
        910.0Kbp
        1.4Mbp
        18
        1387586
        1337
        UWI263P
        907.9Kbp
        1.4Mbp
        19
        1409038
        1372
        UWI283P
        903.4Kbp
        1.3Mbp
        16
        1332290
        1277
        XYZ459H
        903.2Kbp
        1.3Mbp
        24
        1272095
        1199
        79.2%
        91.7%
        8.3%
        XYZ459H_kraken2
        79.2%
        91.7%
        8.3%
        roary_pangenome_v5_filtered_nsp
        2115
        1671363
        1833
        roary_pangenome_v5_filtered_sp
        4673
        3347826
        4137
        roary_pangenome_v5_nsp
        2762
        1769304
        1911
        roary_pangenome_v5_nsp-checkpoint
        2762
        1769304
        1911

        QUAST

        Quality assessment tool for genome assemblies.URL: http://quast.bioinf.spbau.ruDOI: 10.1093/bioinformatics/btt086

        Assembly Statistics

        Showing 0/132 rows and 8/8 columns.
        Sample NameN50 (Kbp)L50 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
        B331PP
        903.7Kbp
        0.0K
        903.7Kbp
        1.4Mbp
        24
        932.37
        60.88
        78.8%
        B418PP
        902.8Kbp
        0.0K
        902.8Kbp
        1.4Mbp
        16
        851.29
        51.15
        80.2%
        B500PP
        903.7Kbp
        0.0K
        903.7Kbp
        1.4Mbp
        36
        988.31
        69.57
        82.5%
        ESI26H
        910.4Kbp
        0.0K
        910.4Kbp
        1.3Mbp
        14
        488.39
        31.81
        72.9%
        ESI36H
        909.9Kbp
        0.0K
        909.9Kbp
        1.2Mbp
        14
        738.26
        33.18
        72.1%
        ESI403H
        910.4Kbp
        0.0K
        910.4Kbp
        1.4Mbp
        10
        541.99
        35.63
        83.1%
        ESI425H
        342.8Kbp
        0.0K
        434.8Kbp
        1.3Mbp
        12
        813.35
        39.89
        73.8%
        GCA_002151465.1_ASM215146v1_genomic
        909.9Kbp
        0.0K
        909.9Kbp
        1.3Mbp
        1
        44.27
        10.74
        82.7%
        GCA_002151485.1_ASM215148v1_genomic
        910.7Kbp
        0.0K
        910.7Kbp
        1.3Mbp
        4
        110.48
        14.05
        83.1%
        GCA_002151505.1_ASM215150v1_genomic
        909.9Kbp
        0.0K
        909.9Kbp
        1.3Mbp
        2
        93.47
        15.29
        85.5%
        GCA_002442595.2_ASM244259v2_genomic
        903.7Kbp
        0.0K
        903.7Kbp
        1.4Mbp
        24
        932.37
        60.88
        78.8%
        GCA_003367295.1_ASM336729v1_genomic
        908.5Kbp
        0.0K
        908.5Kbp
        1.3Mbp
        16
        758.69
        44.05
        75.0%
        GCA_019134655.1_ASM1913465v1_genomic
        910.0Kbp
        0.0K
        910.0Kbp
        1.2Mbp
        13
        837.36
        39.56
        73.3%
        GCA_019464575.1_ASM1946457v1_genomic
        903.7Kbp
        0.0K
        903.7Kbp
        1.4Mbp
        30
        948.06
        69.76
        81.1%
        GCA_024662155.1_ASM2466215v1_genomic
        903.2Kbp
        0.0K
        903.2Kbp
        1.4Mbp
        23
        892.56
        59.71
        79.5%
        GCA_024662175.1_ASM2466217v1_genomic
        920.8Kbp
        0.0K
        920.8Kbp
        1.4Mbp
        18
        844.86
        51.95
        78.7%
        GCA_024662195.1_ASM2466219v1_genomic
        909.7Kbp
        0.0K
        909.7Kbp
        1.5Mbp
        0
        1.98
        4.36
        99.4%
        GCA_030439605.1_ASM3043960v1_genomic
        910.7Kbp
        0.0K
        910.7Kbp
        1.0Mbp
        0
        3.28
        3.37
        66.2%
        GCA_030439625.1_ASM3043962v1_genomic
        910.4Kbp
        0.0K
        910.4Kbp
        1.0Mbp
        1
        331.98
        17.27
        66.2%
        GCA_030439665.1_ASM3043966v1_genomic
        902.8Kbp
        0.0K
        902.8Kbp
        1.0Mbp
        1
        551.26
        21.27
        65.6%
        GCA_030440345.1_ASM3044034v1_genomic
        907.8Kbp
        0.0K
        907.8Kbp
        1.0Mbp
        1
        529.06
        19.61
        65.4%
        GCA_030444985.1_ASM3044498v1_genomic
        910.6Kbp
        0.0K
        910.6Kbp
        1.0Mbp
        0
        8.73
        4.07
        66.2%
        GCA_030445005.1_ASM3044500v1_genomic
        910.4Kbp
        0.0K
        910.4Kbp
        1.0Mbp
        1
        331.98
        17.17
        66.2%
        GCA_030445025.1_ASM3044502v1_genomic
        910.7Kbp
        0.0K
        910.7Kbp
        1.0Mbp
        1
        337.59
        16.97
        66.2%
        GCA_030445065.1_ASM3044506v1_genomic
        910.2Kbp
        0.0K
        910.2Kbp
        1.0Mbp
        1
        286.20
        12.82
        66.1%
        GCA_032595375.1_ASM3259537v1_genomic
        909.6Kbp
        0.0K
        909.6Kbp
        1.0Mbp
        1
        347.73
        17.68
        66.2%
        GCA_032595515.1_ASM3259551v1_genomic
        911.4Kbp
        0.0K
        911.4Kbp
        1.0Mbp
        2
        338.46
        17.20
        65.2%
        GCA_032595535.1_ASM3259553v1_genomic
        909.7Kbp
        0.0K
        909.7Kbp
        1.0Mbp
        2
        569.01
        19.27
        64.8%
        GCA_032595755.1_ASM3259575v1_genomic
        910.1Kbp
        0.0K
        910.1Kbp
        1.0Mbp
        0
        586.83
        24.44
        62.7%
        GCA_038801875.1_ASM3880187v1_genomic
        920.0Kbp
        0.0K
        920.0Kbp
        0.9Mbp
        1
        522.63
        18.34
        62.0%
        GCA_040790715.1_ASM4079071v1_genomic
        908.7Kbp
        0.0K
        908.7Kbp
        1.3Mbp
        20
        730.03
        47.72
        77.2%
        GCA_040790735.1_ASM4079073v1_genomic
        909.5Kbp
        0.0K
        909.5Kbp
        1.4Mbp
        20
        833.46
        45.12
        78.7%
        GCA_040790745.1_ASM4079074v1_genomic
        902.8Kbp
        0.0K
        902.8Kbp
        1.4Mbp
        18
        860.85
        53.89
        81.0%
        GCA_040790755.1_ASM4079075v1_genomic
        902.7Kbp
        0.0K
        902.7Kbp
        1.3Mbp
        21
        838.73
        53.63
        80.8%
        GCA_040790765.1_ASM4079076v1_genomic
        910.1Kbp
        0.0K
        910.1Kbp
        1.4Mbp
        16
        832.72
        44.26
        77.7%
        GCA_040790775.1_ASM4079077v1_genomic
        907.6Kbp
        0.0K
        907.6Kbp
        1.4Mbp
        4
        1.06
        3.96
        92.9%
        GCA_040790785.1_ASM4079078v1_genomic
        910.0Kbp
        0.0K
        910.0Kbp
        1.4Mbp
        14
        813.36
        47.49
        78.8%
        GCA_040790795.1_ASM4079079v1_genomic
        916.8Kbp
        0.0K
        916.8Kbp
        1.3Mbp
        15
        684.36
        44.78
        76.1%
        GCA_040790805.1_ASM4079080v1_genomic
        907.9Kbp
        0.0K
        907.9Kbp
        1.2Mbp
        4
        51.83
        13.27
        79.7%
        GCA_040819585.1_PFhe_I_PB_Ill_cons_genomic
        910.3Kbp
        0.0K
        910.3Kbp
        1.3Mbp
        4
        525.65
        34.93
        78.5%
        GCF_000008685.2_ASM868v2_genomic
        910.7Kbp
        0.0K
        910.7Kbp
        1.5Mbp
        0
        0.00
        0.00
        100.0%
        GCF_000021405.1_ASM2140v1_genomic
        906.7Kbp
        0.0K
        906.7Kbp
        1.3Mbp
        7
        511.34
        38.10
        83.3%
        GCF_000166635.1_ASM16663v1_genomic
        902.2Kbp
        0.0K
        902.2Kbp
        1.3Mbp
        15
        825.88
        48.73
        79.1%
        GCF_000166655.1_ASM16665v1_genomic
        922.8Kbp
        0.0K
        922.8Kbp
        1.5Mbp
        29
        992.45
        62.44
        80.6%
        GCF_000171735.2_ASM17173v2_genomic
        85.3Kbp
        0.0K
        231.4Kbp
        1.5Mbp
        16
        811.09
        42.01
        78.2%
        GCF_000172295.2_ASM17229v2_genomic
        35.7Kbp
        0.0K
        88.9Kbp
        1.3Mbp
        9
        850.71
        63.80
        77.5%
        GCF_000172315.2_ASM17231v2_genomic
        83.1Kbp
        0.0K
        209.2Kbp
        1.3Mbp
        9
        697.00
        38.81
        74.4%
        GCF_000172335.2_ASM17233v2_genomic
        169.2Kbp
        0.0K
        408.6Kbp
        1.5Mbp
        12
        444.76
        34.50
        88.2%
        GCF_000181555.2_ASM18155v2_genomic
        908.8Kbp
        0.0K
        908.8Kbp
        1.5Mbp
        18
        881.52
        57.29
        79.3%
        GCF_000181575.2_ASM18157v2_genomic
        171.0Kbp
        0.0K
        471.2Kbp
        1.3Mbp
        10
        571.41
        34.76
        77.4%
        GCF_000181715.2_ASM18171v2_genomic
        169.5Kbp
        0.0K
        216.3Kbp
        1.3Mbp
        16
        778.57
        42.03
        76.3%
        GCF_000181855.2_ASM18185v2_genomic
        37.0Kbp
        0.0K
        147.8Kbp
        1.4Mbp
        24
        939.06
        76.21
        80.4%
        GCF_002151465.1_ASM215146v1_genomic
        909.9Kbp
        0.0K
        909.9Kbp
        1.3Mbp
        1
        44.27
        10.74
        82.7%
        GCF_002151485.1_ASM215148v1_genomic
        910.7Kbp
        0.0K
        910.7Kbp
        1.3Mbp
        4
        110.48
        14.05
        83.1%
        GCF_002151505.1_ASM215150v1_genomic
        909.9Kbp
        0.0K
        909.9Kbp
        1.3Mbp
        2
        93.47
        15.29
        85.5%
        GCF_002442595.2_ASM244259v2_genomic
        903.7Kbp
        0.0K
        903.7Kbp
        1.4Mbp
        24
        932.37
        60.88
        78.8%
        GCF_003367295.1_ASM336729v1_genomic
        908.5Kbp
        0.0K
        908.5Kbp
        1.3Mbp
        16
        758.69
        44.05
        75.0%
        GCF_019134655.1_ASM1913465v1_genomic
        910.0Kbp
        0.0K
        910.0Kbp
        1.2Mbp
        13
        837.36
        39.56
        73.3%
        GCF_019464575.1_ASM1946457v1_genomic
        903.7Kbp
        0.0K
        903.7Kbp
        1.4Mbp
        30
        948.06
        69.76
        81.1%
        GCF_024662155.1_ASM2466215v1_genomic
        903.2Kbp
        0.0K
        903.2Kbp
        1.4Mbp
        23
        892.56
        59.71
        79.5%
        GCF_024662175.1_ASM2466217v1_genomic
        920.8Kbp
        0.0K
        920.8Kbp
        1.4Mbp
        18
        844.86
        51.95
        78.7%
        GCF_024662195.1_ASM2466219v1_genomic
        909.7Kbp
        0.0K
        909.7Kbp
        1.5Mbp
        0
        1.98
        4.36
        99.4%
        GCF_040790715.1_ASM4079071v1_genomic
        908.7Kbp
        0.0K
        908.7Kbp
        1.3Mbp
        20
        730.03
        47.72
        77.2%
        GCF_040790735.1_ASM4079073v1_genomic
        909.5Kbp
        0.0K
        909.5Kbp
        1.4Mbp
        20
        833.46
        45.12
        78.7%
        GCF_040790745.1_ASM4079074v1_genomic
        902.8Kbp
        0.0K
        902.8Kbp
        1.4Mbp
        18
        860.85
        53.89
        81.0%
        GCF_040790755.1_ASM4079075v1_genomic
        902.7Kbp
        0.0K
        902.7Kbp
        1.3Mbp
        21
        838.73
        53.63
        80.8%
        GCF_040790765.1_ASM4079076v1_genomic
        910.1Kbp
        0.0K
        910.1Kbp
        1.4Mbp
        16
        832.72
        44.26
        77.7%
        GCF_040790775.1_ASM4079077v1_genomic
        907.6Kbp
        0.0K
        907.6Kbp
        1.4Mbp
        4
        1.06
        3.96
        92.9%
        GCF_040790785.1_ASM4079078v1_genomic
        910.0Kbp
        0.0K
        910.0Kbp
        1.4Mbp
        14
        813.36
        47.49
        78.8%
        GCF_040790795.1_ASM4079079v1_genomic
        916.8Kbp
        0.0K
        916.8Kbp
        1.3Mbp
        15
        684.36
        44.78
        76.1%
        GCF_040790805.1_ASM4079080v1_genomic
        907.9Kbp
        0.0K
        907.9Kbp
        1.2Mbp
        4
        51.83
        13.27
        79.7%
        GCF_040819585.1_PFhe_I_PB_Ill_cons_genomic
        910.3Kbp
        0.0K
        910.3Kbp
        1.3Mbp
        4
        525.65
        34.93
        78.5%
        K89HH
        274.3Kbp
        0.0K
        552.7Kbp
        1.5Mbp
        20
        794.74
        55.63
        85.1%
        UCT109H
        910.6Kbp
        0.0K
        910.6Kbp
        1.5Mbp
        12
        119.40
        16.16
        93.1%
        UCT110H
        906.8Kbp
        0.0K
        906.8Kbp
        1.4Mbp
        18
        747.51
        42.21
        78.0%
        UCT113H
        905.8Kbp
        0.0K
        905.8Kbp
        1.3Mbp
        19
        683.13
        35.66
        75.1%
        UCT124H
        900.9Kbp
        0.0K
        900.9Kbp
        1.5Mbp
        9
        405.69
        34.88
        90.0%
        UCT29H
        910.5Kbp
        0.0K
        910.5Kbp
        1.6Mbp
        19
        224.26
        28.36
        97.1%
        UCT30H
        905.5Kbp
        0.0K
        905.5Kbp
        1.5Mbp
        30
        777.99
        55.55
        79.2%
        UCT31H
        910.6Kbp
        0.0K
        910.6Kbp
        1.5Mbp
        16
        228.94
        28.73
        94.2%
        UCT32H
        921.1Kbp
        0.0K
        921.1Kbp
        1.5Mbp
        28
        932.44
        58.02
        80.1%
        UCT35H
        910.0Kbp
        0.0K
        910.0Kbp
        1.3Mbp
        19
        684.11
        34.37
        74.8%
        UCT50H
        902.8Kbp
        0.0K
        902.8Kbp
        1.3Mbp
        16
        796.43
        55.42
        78.5%
        UCT92H
        906.7Kbp
        0.0K
        906.7Kbp
        1.5Mbp
        29
        909.46
        55.27
        80.0%
        UCT95H
        893.6Kbp
        0.0K
        893.6Kbp
        1.5Mbp
        20
        917.34
        850.00
        74.4%
        UCT96H
        900.9Kbp
        0.0K
        900.9Kbp
        1.5Mbp
        20
        434.17
        32.70
        90.8%
        UNY1032P
        910.6Kbp
        0.0K
        910.6Kbp
        1.5Mbp
        3
        88.25
        15.50
        93.7%
        UNY1038P
        915.7Kbp
        0.0K
        915.7Kbp
        1.4Mbp
        18
        743.29
        45.05
        78.4%
        UNY1083P
        923.1Kbp
        0.0K
        923.1Kbp
        1.4Mbp
        28
        795.09
        55.07
        80.3%
        UNY1085P
        903.4Kbp
        0.0K
        903.4Kbp
        1.4Mbp
        19
        878.26
        57.40
        79.8%
        UNY1090P
        912.7Kbp
        0.0K
        912.7Kbp
        1.4Mbp
        17
        827.41
        42.21
        79.0%
        UNY1128P
        213.8Kbp
        0.0K
        709.5Kbp
        1.4Mbp
        27
        828.82
        65.41
        81.7%
        UNY149P
        915.7Kbp
        0.0K
        915.7Kbp
        1.4Mbp
        21
        841.47
        49.76
        80.0%
        UNY169P
        902.8Kbp
        0.0K
        902.8Kbp
        1.3Mbp
        18
        855.10
        53.06
        80.4%
        UNY172P
        903.4Kbp
        0.0K
        903.4Kbp
        1.4Mbp
        17
        841.18
        53.26
        79.0%
        UNY193P
        910.1Kbp
        0.0K
        910.1Kbp
        1.4Mbp
        10
        769.19
        46.76
        77.0%
        UNY203P
        910.1Kbp
        0.0K
        910.1Kbp
        1.3Mbp
        15
        731.32
        33.69
        74.6%
        UNY208P
        912.7Kbp
        0.0K
        912.7Kbp
        1.4Mbp
        14
        772.90
        41.67
        78.5%
        UNY990P
        902.8Kbp
        0.0K
        902.8Kbp
        1.4Mbp
        14
        807.88
        53.28
        78.8%
        URI101H
        910.5Kbp
        0.0K
        910.5Kbp
        1.6Mbp
        18
        200.18
        22.77
        94.4%
        URI102H
        910.6Kbp
        0.0K
        910.6Kbp
        1.4Mbp
        10
        92.81
        11.59
        91.2%
        URI103H
        921.1Kbp
        0.0K
        921.1Kbp
        1.5Mbp
        25
        869.46
        52.92
        80.5%
        URI107H
        910.6Kbp
        0.0K
        910.6Kbp
        1.5Mbp
        12
        127.59
        12.91
        93.0%
        URI111H
        910.6Kbp
        0.0K
        910.6Kbp
        1.5Mbp
        21
        251.16
        28.36
        94.2%
        URI112H
        903.1Kbp
        0.0K
        903.1Kbp
        1.4Mbp
        26
        827.54
        54.85
        79.2%
        URI117H
        434.9Kbp
        0.0K
        461.8Kbp
        1.4Mbp
        16
        738.38
        49.21
        76.7%
        URI118H
        921.0Kbp
        0.0K
        921.0Kbp
        1.4Mbp
        21
        777.62
        48.77
        78.8%
        URI120H
        910.7Kbp
        0.0K
        910.7Kbp
        1.6Mbp
        15
        241.92
        30.56
        94.7%
        URI33H
        902.8Kbp
        0.0K
        902.8Kbp
        1.3Mbp
        18
        777.30
        49.44
        79.8%
        URI34H
        910.1Kbp
        0.0K
        910.1Kbp
        1.4Mbp
        9
        704.15
        41.21
        75.9%
        URI36H
        927.7Kbp
        0.0K
        927.7Kbp
        1.5Mbp
        39
        973.06
        63.98
        82.6%
        URI39H
        920.7Kbp
        0.0K
        920.7Kbp
        1.6Mbp
        15
        216.20
        22.67
        96.5%
        URI40H
        910.6Kbp
        0.0K
        910.6Kbp
        1.5Mbp
        15
        147.59
        20.18
        93.4%
        URI41H
        914.4Kbp
        0.0K
        914.4Kbp
        1.5Mbp
        13
        166.82
        22.52
        91.7%
        URI42H
        910.6Kbp
        0.0K
        910.6Kbp
        1.5Mbp
        12
        153.47
        20.25
        90.3%
        URI44H
        921.1Kbp
        0.0K
        921.1Kbp
        1.4Mbp
        24
        798.63
        51.27
        78.8%
        URI45H
        42.8Kbp
        0.0K
        254.7Kbp
        1.5Mbp
        21
        859.07
        53.87
        80.8%
        URI46H
        906.8Kbp
        0.0K
        906.8Kbp
        1.4Mbp
        29
        817.66
        52.04
        79.3%
        URI47H
        921.2Kbp
        0.0K
        921.2Kbp
        1.5Mbp
        31
        924.47
        58.01
        80.9%
        URI48H
        902.8Kbp
        0.0K
        902.8Kbp
        1.4Mbp
        18
        854.78
        48.47
        79.7%
        URI56H
        903.3Kbp
        0.0K
        903.3Kbp
        1.3Mbp
        14
        728.86
        48.69
        77.9%
        URI86H
        919.1Kbp
        0.0K
        919.1Kbp
        1.4Mbp
        24
        763.12
        43.83
        78.0%
        URI87H
        910.6Kbp
        0.0K
        910.6Kbp
        1.5Mbp
        12
        152.86
        15.37
        93.8%
        URI88H
        906.7Kbp
        0.0K
        906.7Kbp
        1.5Mbp
        34
        919.68
        56.37
        81.5%
        URI89H
        910.7Kbp
        0.0K
        910.7Kbp
        1.5Mbp
        17
        195.47
        23.38
        94.1%
        URI91H
        910.7Kbp
        0.0K
        910.7Kbp
        1.6Mbp
        12
        114.59
        13.08
        96.1%
        URI93H
        910.6Kbp
        0.0K
        910.6Kbp
        1.5Mbp
        15
        137.80
        21.54
        93.4%
        UWI247P
        912.3Kbp
        0.0K
        912.3Kbp
        1.4Mbp
        16
        747.05
        44.21
        76.9%
        UWI248P
        910.0Kbp
        0.0K
        910.0Kbp
        1.4Mbp
        18
        784.23
        52.06
        77.0%
        UWI263P
        907.9Kbp
        0.0K
        907.9Kbp
        1.4Mbp
        25
        829.11
        51.82
        78.6%
        UWI283P
        903.4Kbp
        0.0K
        903.4Kbp
        1.3Mbp
        20
        872.33
        51.52
        77.2%
        XYZ459H
        903.2Kbp
        0.0K
        903.2Kbp
        1.3Mbp
        8
        757.97
        44.71
        75.2%

        Number of Contigs

        This plot shows the number of contigs found for each assembly, broken down by length.

        Created with MultiQC

        Bakta

        Version: 1.10.0

        Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.URL: https://github.com/oschwengers/baktaDOI: 10.1099/mgen.0.000685

        This barplot shows the distribution of different types of features found in each sample.

        Bakta can detect different features:

        • tRNAs
        • tmRNAs
        • rRNAs
        • ncRNAs
        • ncRNA regions
        • CRISPR arrays
        • CDSs
        • pseudogenes
        • hypotheticals
        • signal peptides
        • sORFs
        • gaps
        • oriCs
        • oriVs
        • oriTs

        This barplot shows you the distribution of these different types of features found in each sample.

        Created with MultiQC

        Kraken

        Taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.URL: https://ccb.jhu.edu/software/krakenDOI: 10.1186/gb-2014-15-3-r46

        Top taxa

        The number of reads falling into the top 5 taxa across different ranks.

        To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top 5 taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.

        The total number of reads is approximated by dividing the number of unclassified reads by the percentage of the library that they account for. Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.

        The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.

        Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Bakta1.10.0